rs716501

chr4-122430770-G-Achr4-122430770-G-Cchr4-122430770-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.29 in 151,946 control chromosomes in the GnomAD database, including 7,536 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44048 AN: 151828 Hom.: 7535 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 44050 AN: 151946 Hom.: 7536 Cov.: 32 AF XY: 0.297 AC XY: 22045 AN XY: 74254

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.271

Alfa AF: 0.322 Hom.: 4584

Bravo AF: 0.280

Asia WGS AF: 0.298 AC: 1031 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.79
Dann	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs716501; hg19: chr4-123351925;